def get_predictions_accounting_for_centering(self,
cb_op_to_primitive=None,
**kwargs):
# interface requires this function to set current_orientation
# in the actual setting used for Miller index calculation
if (self.horizons_phil.known_setting is None or self.horizons_phil.known_setting == self.setting_id ) and \
self.horizons_phil.integration.model in ["use_case_3_simulated_annealing",
"use_case_3_simulated_annealing_7",
"use_case_3_simulated_annealing_9"]:
if cb_op_to_primitive == None:
raise Sorry(
"Can't use model_3 simulated annealing for non-primitive cells, contact authors."
)
if self.horizons_phil.integration.model == "use_case_3_simulated_annealing":
self.best_params = dict(
zip(("half_mosaicity_deg", "wave_HE_ang", "wave_LE_ang",
"reserve_orientation", "rotation100_rad",
"rotation010_rad", "rotation001_rad"),
self.use_case_3_simulated_annealing(
self.horizons_phil.integration.
use_subpixel_translations)))
elif self.horizons_phil.integration.model == "use_case_3_simulated_annealing_7":
self.best_params = dict(
zip(("half_mosaicity_deg", "wave_HE_ang", "wave_LE_ang",
"reserve_orientation", "rotation100_rad",
"rotation010_rad", "rotation001_rad",
"domain_size_ang"),
self.use_case_3_simulated_annealing_7(
self.horizons_phil.integration.
use_subpixel_translations)))
elif self.horizons_phil.integration.model == "use_case_3_simulated_annealing_9":
self.best_params = dict(
zip(("half_mosaicity_deg", "wave_HE_ang", "wave_LE_ang",
"reserve_orientation", "rotation100_rad",
"rotation010_rad", "rotation001_rad",
"domain_size_ang", "ab_factor", "c_factor"),
self.use_case_3_simulated_annealing_9(
self.horizons_phil.integration.
use_subpixel_translations)))
self.current_orientation = self.best_params["reserve_orientation"]
self.current_cb_op_to_primitive = cb_op_to_primitive
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format(
)
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.predicted, self.hkllist = BPpredicted, BPhkllist
self.partialities = dict(
indices=BPhkllist.deep_copy(),
data=self.bp3_wrapper.ucbp3.selected_partialities())
#self.hi = self.bp3_wrapper.ucbp3.selected_hi_predictions()
#self.lo = self.bp3_wrapper.ucbp3.selected_lo_predictions()
#print list(self.partialities)
#for x in range(len(self.hi)):
# print "%4d %4d %4d %7.1f %7.1f %7.1f %7.1f PARTIAL %7.2f"%(
# self.hkllist[x][0], self.hkllist[x][1],self.hkllist[x][2],
# self.hi[x][0], self.hi[x][1],
# self.lo[x][0], self.lo[x][1], self.partialities[x])
if self.inputai.active_areas != None:
self.predicted, self.hkllist = self.inputai.active_areas(
self.predicted, self.hkllist, self.pixel_size)
return
if self.horizons_phil.integration.model == "user_supplied":
lower_limit_domain_size = math.pow(
self.inputai.getOrientation().unit_cell().volume(), 1. / 3.
) * self.horizons_phil.integration.mosaic.domain_size_lower_limit # default 10-unit cell block size minimum reasonable domain
actual_used_domain_size = kwargs.get("domain_size_ang",
lower_limit_domain_size)
if cb_op_to_primitive == None:
from cxi_user import pre_get_predictions
self.bp3_wrapper = pre_get_predictions(
self.inputai,
self.horizons_phil,
raw_image=self.imagefiles.images[self.image_number],
imageindex=self.frame_numbers[self.image_number],
spotfinder=self.spotfinder,
limiting_resolution=self.limiting_resolution,
domain_size_ang=actual_used_domain_size)
self.current_orientation = self.inputai.getOrientation()
self.current_cb_op_to_primitive = cb_op_to_primitive
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format(
)
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.predicted, self.hkllist = BPpredicted, BPhkllist
if self.inputai.active_areas != None:
self.predicted, self.hkllist = self.inputai.active_areas(
self.predicted, self.hkllist, self.pixel_size)
return
else:
self.block_counter += 1
rot_mat = matrix.sqr(
cb_op_to_primitive.c().r().as_double()).transpose()
centered_orientation = self.inputai.getOrientation()
self.current_orientation = centered_orientation
self.current_cb_op_to_primitive = cb_op_to_primitive
primitive_orientation = centered_orientation.change_basis(
rot_mat)
self.inputai.setOrientation(primitive_orientation)
from cxi_user import pre_get_predictions
if self.block_counter < 2:
KLUDGE = self.horizons_phil.integration.mosaic.kludge1 # bugfix 1 of 2 for protocol 6, equation 2
self.inputai.setMosaicity(KLUDGE *
self.inputai.getMosaicity())
self.bp3_wrapper = pre_get_predictions(
self.inputai,
self.horizons_phil,
raw_image=self.imagefiles.images[self.image_number],
imageindex=self.frame_numbers[self.image_number],
spotfinder=self.spotfinder,
limiting_resolution=self.limiting_resolution,
domain_size_ang=actual_used_domain_size)
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format(
)
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.actual = actual_used_domain_size
self.predicted = BPpredicted
primitive_hkllist = BPhkllist
#not sure if matrix needs to be transposed first for outputting HKL's???:
self.hkllist = cb_op_to_primitive.inverse().apply(
primitive_hkllist)
self.inputai.setOrientation(centered_orientation)
if self.inputai.active_areas != None:
self.predicted, self.hkllist = self.inputai.active_areas(
self.predicted, self.hkllist, self.pixel_size)
if self.block_counter < 2:
down = self.inputai.getMosaicity() / KLUDGE
print "Readjusting mosaicity back down to ", down
self.inputai.setMosaicity(down)
return
if cb_op_to_primitive == None:
predicted = self.inputai.predict_all(
self.image_centers[self.image_number],
self.limiting_resolution)
self.predicted = predicted.vec3(
) #only good for integrating one frame...
self.hkllist = predicted.hkl()
self.current_orientation = self.inputai.getOrientation()
from cctbx import sgtbx
self.cb_op_to_primitive = sgtbx.change_of_basis_op()
else:
rot_mat = matrix.sqr(
cb_op_to_primitive.c().r().as_double()).transpose()
centered_orientation = self.inputai.getOrientation()
self.current_orientation = centered_orientation
self.current_cb_op_to_primitive = cb_op_to_primitive
primitive_orientation = centered_orientation.change_basis(rot_mat)
self.inputai.setOrientation(primitive_orientation)
predicted = self.inputai.predict_all(
self.image_centers[self.image_number],
self.limiting_resolution)
self.predicted = predicted.vec3(
) #only good for integrating one frame...
primitive_hkllist = predicted.hkl()
#not sure if matrix needs to be transposed first for outputting HKL's???:
self.hkllist = cb_op_to_primitive.inverse().apply(
primitive_hkllist)
self.inputai.setOrientation(centered_orientation)
if self.inputai.active_areas != None:
self.predicted, self.hkllist = self.inputai.active_areas(
self.predicted, self.hkllist, self.pixel_size)
if False: #development only; compare the two methods:
from matplotlib import pyplot as plt
plt.plot([i[0] for i in BPpredicted], [i[1] for i in BPpredicted],
"r.")
plt.plot([i[0] for i in predicted], [i[1] for i in predicted],
"b.")
plt.show()
def get_predictions_accounting_for_centering(self,experiments,reflections,cb_op_to_primitive,**kwargs):
# interface requires this function to set current_orientation
# in the actual setting used for Miller index calculation
detector = experiments[0].detector
crystal = experiments[0].crystal
if self.horizons_phil.integration.model == "user_supplied":
lower_limit_domain_size = math.pow(
crystal.get_unit_cell().volume(),
1./3.)*self.horizons_phil.integration.mosaic.domain_size_lower_limit # default 10-unit cell block size minimum reasonable domain
actual_used_domain_size = kwargs.get("domain_size_ang",lower_limit_domain_size)
self.block_counter+=1
rot_mat = matrix.sqr(cb_op_to_primitive.c().r().as_double()).transpose()
from cctbx.crystal_orientation import crystal_orientation, basis_type
centered_orientation = crystal_orientation(crystal.get_A(),basis_type.reciprocal)
self.current_orientation = centered_orientation
self.current_cb_op_to_primitive = cb_op_to_primitive
primitive_orientation = centered_orientation.change_basis(rot_mat)
self.inputai.setOrientation(primitive_orientation)
from cxi_user import pre_get_predictions
if self.block_counter < 2:
KLUDGE = self.horizons_phil.integration.mosaic.kludge1 # bugfix 1 of 2 for protocol 6, equation 2
self.inputai.setMosaicity(KLUDGE*self.inputai.getMosaicity())
oldbase = self.inputai.getBase()
#print oldbase.xbeam, oldbase.ybeam
newbeam = detector[0].get_beam_centre(experiments[0].beam.get_s0())
newdistance = -detector[0].get_beam_centre_lab(experiments[0].beam.get_s0())[2]
from labelit.dptbx import Parameters
base = Parameters(xbeam = newbeam[0], ybeam = newbeam[1], #oldbase.xbeam, ybeam = oldbase.ybeam,
distance = newdistance, twotheta = 0.0)
self.inputai.setBase(base)
self.inputai.setWavelength(experiments[0].beam.get_wavelength())
self.bp3_wrapper = pre_get_predictions(self.inputai, self.horizons_phil,
raw_image = self.imagefiles.images[self.image_number],
imageindex = self.frame_numbers[self.image_number],
spotfinder = self.spotfinder,
limiting_resolution = self.limiting_resolution,
domain_size_ang = actual_used_domain_size,
)
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format()
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.actual = actual_used_domain_size
primitive_hkllist = BPhkllist
#not sure if matrix needs to be transposed first for outputting HKL's???:
self.hkllist = cb_op_to_primitive.inverse().apply(primitive_hkllist)
if self.horizons_phil.integration.spot_prediction == "dials":
from dials.algorithms.spot_prediction import StillsReflectionPredictor
predictor = StillsReflectionPredictor(experiments[0])
Rcalc = flex.reflection_table.empty_standard(len(self.hkllist))
Rcalc['miller_index'] = self.hkllist
predictor.for_reflection_table(Rcalc, crystal.get_A())
self.predicted = Rcalc['xyzcal.mm']
self.dials_spot_prediction = Rcalc
self.dials_model = experiments
elif self.horizons_phil.integration.spot_prediction == "ucbp3":
self.predicted = BPpredicted
self.inputai.setOrientation(centered_orientation)
if self.inputai.active_areas != None:
self.predicted,self.hkllist = self.inputai.active_areas(
self.predicted,self.hkllist,self.pixel_size)
if self.block_counter < 2:
down = self.inputai.getMosaicity()/KLUDGE
print "Readjusting mosaicity back down to ",down
self.inputai.setMosaicity(down)
return
def get_predictions_accounting_for_centering(self, experiments,
reflections,
cb_op_to_primitive, **kwargs):
# interface requires this function to set current_orientation
# in the actual setting used for Miller index calculation
detector = experiments[0].detector
crystal = experiments[0].crystal
if self.horizons_phil.integration.model == "user_supplied":
lower_limit_domain_size = math.pow(
crystal.get_unit_cell().volume(), 1. / 3.
) * self.horizons_phil.integration.mosaic.domain_size_lower_limit # default 10-unit cell block size minimum reasonable domain
actual_used_domain_size = kwargs.get("domain_size_ang",
lower_limit_domain_size)
self.block_counter += 1
rot_mat = matrix.sqr(
cb_op_to_primitive.c().r().as_double()).transpose()
from cctbx.crystal_orientation import crystal_orientation, basis_type
centered_orientation = crystal_orientation(crystal.get_A(),
basis_type.reciprocal)
self.current_orientation = centered_orientation
self.current_cb_op_to_primitive = cb_op_to_primitive
primitive_orientation = centered_orientation.change_basis(rot_mat)
self.inputai.setOrientation(primitive_orientation)
from cxi_user import pre_get_predictions
if self.block_counter < 2:
KLUDGE = self.horizons_phil.integration.mosaic.kludge1 # bugfix 1 of 2 for protocol 6, equation 2
self.inputai.setMosaicity(KLUDGE * self.inputai.getMosaicity())
oldbase = self.inputai.getBase()
#print oldbase.xbeam, oldbase.ybeam
newbeam = detector[0].get_beam_centre(experiments[0].beam.get_s0())
newdistance = -detector[0].get_beam_centre_lab(
experiments[0].beam.get_s0())[2]
from labelit.dptbx import Parameters
base = Parameters(
xbeam=newbeam[0],
ybeam=newbeam[1], #oldbase.xbeam, ybeam = oldbase.ybeam,
distance=newdistance,
twotheta=0.0)
self.inputai.setBase(base)
self.inputai.setWavelength(experiments[0].beam.get_wavelength())
self.bp3_wrapper = pre_get_predictions(
self.inputai,
self.horizons_phil,
raw_image=self.imagefiles.images[self.image_number],
imageindex=self.frame_numbers[self.image_number],
spotfinder=self.spotfinder,
limiting_resolution=self.limiting_resolution,
domain_size_ang=actual_used_domain_size,
)
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format(
)
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.actual = actual_used_domain_size
primitive_hkllist = BPhkllist
#not sure if matrix needs to be transposed first for outputting HKL's???:
self.hkllist = cb_op_to_primitive.inverse().apply(
primitive_hkllist)
if self.horizons_phil.integration.spot_prediction == "dials":
from dials.algorithms.spot_prediction import StillsReflectionPredictor
predictor = StillsReflectionPredictor(experiments[0])
Rcalc = flex.reflection_table.empty_standard(len(self.hkllist))
Rcalc['miller_index'] = self.hkllist
predictor.for_reflection_table(Rcalc, crystal.get_A())
self.predicted = Rcalc['xyzcal.mm']
self.dials_spot_prediction = Rcalc
self.dials_model = experiments
elif self.horizons_phil.integration.spot_prediction == "ucbp3":
self.predicted = BPpredicted
self.inputai.setOrientation(centered_orientation)
if self.inputai.active_areas != None:
self.predicted, self.hkllist = self.inputai.active_areas(
self.predicted, self.hkllist, self.pixel_size)
if self.block_counter < 2:
down = self.inputai.getMosaicity() / KLUDGE
print "Readjusting mosaicity back down to ", down
self.inputai.setMosaicity(down)
return
def get_predictions_accounting_for_centering(self,cb_op_to_primitive=None,**kwargs):
# interface requires this function to set current_orientation
# in the actual setting used for Miller index calculation
if (self.horizons_phil.known_setting is None or self.horizons_phil.known_setting == self.setting_id ) and \
self.horizons_phil.integration.model in ["use_case_3_simulated_annealing",
"use_case_3_simulated_annealing_7",
"use_case_3_simulated_annealing_9"]:
if cb_op_to_primitive==None:
raise Sorry("Can't use model_3 simulated annealing for non-primitive cells, contact authors.")
if self.horizons_phil.integration.model=="use_case_3_simulated_annealing":
self.best_params = dict(zip(("half_mosaicity_deg","wave_HE_ang","wave_LE_ang",
"reserve_orientation","rotation100_rad","rotation010_rad","rotation001_rad"),
self.use_case_3_simulated_annealing(self.horizons_phil.integration.use_subpixel_translations))
)
elif self.horizons_phil.integration.model=="use_case_3_simulated_annealing_7":
self.best_params = dict(zip(("half_mosaicity_deg","wave_HE_ang","wave_LE_ang",
"reserve_orientation","rotation100_rad","rotation010_rad","rotation001_rad",
"domain_size_ang"),
self.use_case_3_simulated_annealing_7(self.horizons_phil.integration.use_subpixel_translations))
)
elif self.horizons_phil.integration.model=="use_case_3_simulated_annealing_9":
self.best_params = dict(zip(("half_mosaicity_deg","wave_HE_ang","wave_LE_ang",
"reserve_orientation","rotation100_rad","rotation010_rad","rotation001_rad",
"domain_size_ang","ab_factor","c_factor"),
self.use_case_3_simulated_annealing_9(self.horizons_phil.integration.use_subpixel_translations))
)
self.current_orientation = self.best_params["reserve_orientation"]
self.current_cb_op_to_primitive = cb_op_to_primitive
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format()
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.predicted,self.hkllist = BPpredicted, BPhkllist
self.partialities = dict(indices=BPhkllist.deep_copy(),
data=self.bp3_wrapper.ucbp3.selected_partialities())
#self.hi = self.bp3_wrapper.ucbp3.selected_hi_predictions()
#self.lo = self.bp3_wrapper.ucbp3.selected_lo_predictions()
#print list(self.partialities)
#for x in xrange(len(self.hi)):
# print "%4d %4d %4d %7.1f %7.1f %7.1f %7.1f PARTIAL %7.2f"%(
# self.hkllist[x][0], self.hkllist[x][1],self.hkllist[x][2],
# self.hi[x][0], self.hi[x][1],
# self.lo[x][0], self.lo[x][1], self.partialities[x])
if self.inputai.active_areas != None:
self.predicted,self.hkllist = self.inputai.active_areas(
self.predicted,self.hkllist,self.pixel_size)
return
if self.horizons_phil.integration.model == "user_supplied":
lower_limit_domain_size = math.pow(
self.inputai.getOrientation().unit_cell().volume(),
1./3.)*self.horizons_phil.integration.mosaic.domain_size_lower_limit # default 10-unit cell block size minimum reasonable domain
actual_used_domain_size = kwargs.get("domain_size_ang",lower_limit_domain_size)
if cb_op_to_primitive==None:
from cxi_user import pre_get_predictions
self.bp3_wrapper = pre_get_predictions(self.inputai, self.horizons_phil,
raw_image = self.imagefiles.images[self.image_number],
imageindex = self.frame_numbers[self.image_number],
spotfinder = self.spotfinder,
limiting_resolution = self.limiting_resolution,
domain_size_ang = actual_used_domain_size)
self.current_orientation = self.inputai.getOrientation()
self.current_cb_op_to_primitive = cb_op_to_primitive
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format()
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.predicted,self.hkllist = BPpredicted, BPhkllist
if self.inputai.active_areas != None:
self.predicted,self.hkllist = self.inputai.active_areas(
self.predicted,self.hkllist,self.pixel_size)
return
else:
self.block_counter+=1
rot_mat = matrix.sqr(cb_op_to_primitive.c().r().as_double()).transpose()
centered_orientation = self.inputai.getOrientation()
self.current_orientation = centered_orientation
self.current_cb_op_to_primitive = cb_op_to_primitive
primitive_orientation = centered_orientation.change_basis(rot_mat)
self.inputai.setOrientation(primitive_orientation)
from cxi_user import pre_get_predictions
if self.block_counter < 2:
KLUDGE = self.horizons_phil.integration.mosaic.kludge1 # bugfix 1 of 2 for protocol 6, equation 2
self.inputai.setMosaicity(KLUDGE*self.inputai.getMosaicity())
self.bp3_wrapper = pre_get_predictions(self.inputai, self.horizons_phil,
raw_image = self.imagefiles.images[self.image_number],
imageindex = self.frame_numbers[self.image_number],
spotfinder = self.spotfinder,
limiting_resolution = self.limiting_resolution,
domain_size_ang = actual_used_domain_size)
BPpredicted = self.bp3_wrapper.ucbp3.selected_predictions_labelit_format()
BPhkllist = self.bp3_wrapper.ucbp3.selected_hkls()
self.actual = actual_used_domain_size
self.predicted = BPpredicted
primitive_hkllist = BPhkllist
#not sure if matrix needs to be transposed first for outputting HKL's???:
self.hkllist = cb_op_to_primitive.inverse().apply(primitive_hkllist)
self.inputai.setOrientation(centered_orientation)
if self.inputai.active_areas != None:
self.predicted,self.hkllist = self.inputai.active_areas(
self.predicted,self.hkllist,self.pixel_size)
if self.block_counter < 2:
down = self.inputai.getMosaicity()/KLUDGE
print "Readjusting mosaicity back down to ",down
self.inputai.setMosaicity(down)
return
if cb_op_to_primitive==None:
predicted = self.inputai.predict_all(
self.image_centers[self.image_number],self.limiting_resolution)
self.predicted = predicted.vec3() #only good for integrating one frame...
self.hkllist = predicted.hkl()
self.current_orientation = self.inputai.getOrientation()
from cctbx import sgtbx
self.cb_op_to_primitive = sgtbx.change_of_basis_op()
else:
rot_mat = matrix.sqr(cb_op_to_primitive.c().r().as_double()).transpose()
centered_orientation = self.inputai.getOrientation()
self.current_orientation = centered_orientation
self.current_cb_op_to_primitive = cb_op_to_primitive
primitive_orientation = centered_orientation.change_basis(rot_mat)
self.inputai.setOrientation(primitive_orientation)
predicted = self.inputai.predict_all(
self.image_centers[self.image_number],self.limiting_resolution)
self.predicted = predicted.vec3() #only good for integrating one frame...
primitive_hkllist = predicted.hkl()
#not sure if matrix needs to be transposed first for outputting HKL's???:
self.hkllist = cb_op_to_primitive.inverse().apply(primitive_hkllist)
self.inputai.setOrientation(centered_orientation)
if self.inputai.active_areas != None:
self.predicted,self.hkllist = self.inputai.active_areas(
self.predicted,self.hkllist,self.pixel_size)
if False: #development only; compare the two methods:
from matplotlib import pyplot as plt
plt.plot([i[0] for i in BPpredicted],[i[1] for i in BPpredicted],"r.")
plt.plot([i[0] for i in predicted],[i[1] for i in predicted],"b.")
plt.show()